data_8JA # _chem_comp.id 8JA _chem_comp.name "N-[2,4-bis(oxidanylidene)-1H-pyrimidin-5-yl]-N'-oxidanyl-octanediamide" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H18 N4 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-12-17 _chem_comp.pdbx_modified_date 2024-05-24 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 298.295 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 8JA _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 8JIG _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_ordinal 8JA C10 C1 C 0 1 N N N N N N 63.931 8.967 -11.254 -1.730 0.530 -0.068 C10 8JA 1 8JA C13 C2 C 0 1 N N N N N N 64.947 6.673 -11.113 0.710 0.134 0.120 C13 8JA 2 8JA C15 C3 C 0 1 N N N N N N 63.926 5.896 -8.953 3.172 -0.255 0.302 C15 8JA 3 8JA C17 C4 C 0 1 N N N N N N 63.903 3.864 -7.474 5.633 -0.643 0.484 C17 8JA 4 8JA C02 C5 C 0 1 N N N N N N 62.869 12.234 -11.655 -4.459 -0.670 -0.632 C02 8JA 5 8JA C04 C6 C 0 1 N N N N N N 62.706 13.420 -9.659 -6.563 -0.418 0.355 C04 8JA 6 8JA C07 C7 C 0 1 N N N N N N 62.829 11.079 -9.567 -5.016 1.359 0.503 C07 8JA 7 8JA C08 C8 C 0 1 N N N N N N 62.901 11.031 -10.966 -4.110 0.636 -0.196 C08 8JA 8 8JA C12 C9 C 0 1 N N N N N N 63.734 7.488 -11.506 -0.371 1.036 -0.477 C12 8JA 9 8JA C14 C10 C 0 1 N N N N N N 65.108 6.573 -9.612 2.090 0.647 -0.296 C14 8JA 10 8JA C16 C11 C 0 1 N N N N N N 64.094 4.394 -8.878 4.551 0.259 -0.114 C16 8JA 11 8JA C18 C12 C 0 1 N N N N N N 62.662 4.425 -6.814 6.992 -0.138 0.074 C18 8JA 12 8JA N03 N1 N 0 1 N N N N N N 62.774 13.376 -10.984 -5.682 -1.159 -0.342 N03 8JA 13 8JA N06 N2 N 0 1 N N N N N N 62.733 12.282 -8.952 -6.248 0.820 0.775 N06 8JA 14 8JA N09 N3 N 0 1 N N N N N N 62.997 9.860 -11.615 -2.841 1.169 -0.485 N09 8JA 15 8JA N20 N4 N 0 1 N N N N N N 62.689 5.595 -6.159 8.103 -0.780 0.487 N20 8JA 16 8JA O01 O1 O 0 1 N N N N N N 62.929 12.243 -12.868 -3.664 -1.340 -1.267 O01 8JA 17 8JA O05 O2 O 0 1 N N N N N N 62.620 14.489 -9.088 -7.661 -0.875 0.608 O05 8JA 18 8JA O11 O3 O 0 1 N N N N N N 65.055 9.430 -10.657 -1.825 -0.455 0.634 O11 8JA 19 8JA O19 O4 O 0 1 N N N N N N 61.480 3.763 -6.861 7.086 0.847 -0.627 O19 8JA 20 8JA O21 O5 O 0 1 N N N N N N 63.249 5.670 -4.913 9.380 -0.305 0.102 O21 8JA 21 8JA H1 H1 H 0 1 N N N N N N 64.841 5.659 -11.526 0.632 0.144 1.208 H1 8JA 22 8JA H2 H2 H 0 1 N N N N N N 65.845 7.149 -11.534 0.576 -0.885 -0.244 H2 8JA 23 8JA H3 H3 H 0 1 N N N N N N 63.816 6.291 -7.932 3.093 -0.245 1.389 H3 8JA 24 8JA H4 H4 H 0 1 N N N N N N 63.020 6.122 -9.534 3.038 -1.273 -0.062 H4 8JA 25 8JA H5 H5 H 0 1 N N N N N N 63.816 2.768 -7.518 5.554 -0.633 1.571 H5 8JA 26 8JA H6 H6 H 0 1 N N N N N N 64.780 4.138 -6.870 5.499 -1.662 0.120 H6 8JA 27 8JA H7 H7 H 0 1 N N N N N N 62.850 10.168 -8.987 -4.771 2.354 0.844 H7 8JA 28 8JA H8 H8 H 0 1 N N N N N N 62.870 7.141 -10.920 -0.293 1.026 -1.565 H8 8JA 29 8JA H9 H9 H 0 1 N N N N N N 63.536 7.335 -12.577 -0.237 2.054 -0.113 H9 8JA 30 8JA H10 H10 H 0 1 N N N N N N 66.016 5.993 -9.391 2.169 0.637 -1.383 H10 8JA 31 8JA H11 H11 H 0 1 N N N N N N 65.211 7.587 -9.199 2.224 1.666 0.069 H11 8JA 32 8JA H12 H12 H 0 1 N N N N N N 63.352 3.922 -9.538 4.630 0.248 -1.201 H12 8JA 33 8JA H13 H13 H 0 1 N N N N N N 65.107 4.134 -9.219 4.685 1.277 0.250 H13 8JA 34 8JA H14 H14 H 0 1 N N N N N N 62.753 14.235 -11.496 -5.928 -2.050 -0.637 H14 8JA 35 8JA H16 H16 H 0 1 N N N N N N 62.372 9.653 -12.368 -2.766 1.997 -0.985 H16 8JA 36 8JA H17 H17 H 0 1 N N N N N N 62.299 6.413 -6.582 8.027 -1.568 1.048 H17 8JA 37 8JA H18 H18 H 0 1 N N N N N N 63.188 6.562 -4.591 10.115 -0.830 0.446 H18 8JA 38 8JA H15 H15 H 0 1 N N N N N N 62.681 12.322 -7.954 -6.899 1.337 1.276 H15 8JA 39 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal 8JA O01 C02 DOUB N N 1 8JA C02 N03 SING N N 2 8JA C02 C08 SING N N 3 8JA N09 C10 SING N N 4 8JA N09 C08 SING N N 5 8JA C12 C10 SING N N 6 8JA C12 C13 SING N N 7 8JA C10 O11 DOUB N N 8 8JA C13 C14 SING N N 9 8JA N03 C04 SING N N 10 8JA C08 C07 DOUB N N 11 8JA C04 O05 DOUB N N 12 8JA C04 N06 SING N N 13 8JA C14 C15 SING N N 14 8JA C07 N06 SING N N 15 8JA C15 C16 SING N N 16 8JA C16 C17 SING N N 17 8JA C17 C18 SING N N 18 8JA O19 C18 DOUB N N 19 8JA C18 N20 SING N N 20 8JA N20 O21 SING N N 21 8JA C13 H1 SING N N 22 8JA C13 H2 SING N N 23 8JA C15 H3 SING N N 24 8JA C15 H4 SING N N 25 8JA C17 H5 SING N N 26 8JA C17 H6 SING N N 27 8JA C07 H7 SING N N 28 8JA C12 H8 SING N N 29 8JA C12 H9 SING N N 30 8JA C14 H10 SING N N 31 8JA C14 H11 SING N N 32 8JA C16 H12 SING N N 33 8JA C16 H13 SING N N 34 8JA N03 H14 SING N N 35 8JA N09 H16 SING N N 36 8JA N20 H17 SING N N 37 8JA O21 H18 SING N N 38 8JA N06 H15 SING N N 39 # loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor 8JA InChI InChI 1.03 "InChI=1S/C12H18N4O5/c17-9(5-3-1-2-4-6-10(18)16-21)14-8-7-13-12(20)15-11(8)19/h7,21H,1-6H2,(H,14,17)(H,16,18)(H2,13,15,19,20)" 8JA InChIKey InChI 1.03 XGGQCNFMILXRKW-UHFFFAOYSA-N 8JA SMILES_CANONICAL CACTVS 3.385 "ONC(=O)CCCCCCC(=O)NC1=CNC(=O)NC1=O" 8JA SMILES CACTVS 3.385 "ONC(=O)CCCCCCC(=O)NC1=CNC(=O)NC1=O" 8JA SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=C(C(=O)NC(=O)N1)NC(=O)CCCCCCC(=O)NO" 8JA SMILES "OpenEye OEToolkits" 2.0.7 "C1=C(C(=O)NC(=O)N1)NC(=O)CCCCCCC(=O)NO" # _pdbx_chem_comp_identifier.comp_id 8JA _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "~{N}-[2,4-bis(oxidanylidene)-1~{H}-pyrimidin-5-yl]-~{N}'-oxidanyl-octanediamide" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 8JA "Create component" 2021-12-17 PDBJ 8JA "Modify linking type" 2022-01-18 PDBJ 8JA "Modify name" 2022-01-18 PDBJ 8JA "Modify model coordinates code" 2024-05-20 PDBJ 8JA "Initial release" 2024-05-29 RCSB #